When putting files to the empeg via TCP/IP, you don't have to worry about error correction and resend (That's part of the TCP layer).

With USB you have to do your own packet validation, which slows down the protocol at both ends, and means you have to send more data (all the checksums).
Also (at least in windows) USB has some reserved bandwidth settings (By default, my windows installation reserves 10% of the bandwidth for "system")

Mind you, if you have lots of ethernet devices on your network, you'll likely see a slowdown due to collisions...
YMMV...

Jazz
(List 112, Mk2 12 gig #40. Mk1 4 gig #30. Mk3 1.6 16v)